1. Amino Acids and Proteins 1.What is an amino acid / protein 2.Where are they found 3.Properties of the amino acids 4.How are proteins synthesized 1.Transcription & translation

2. Amino Acids Amine and carboxyl groups. Sidechain ‘R’ is attached to C-alpha carbon The amino acids found in Living organisms are L-amino acids

3. Amino Acids - peptide bond N-terminalC-terminal

4. Transcription & translation DNA |Transcription mRNA | Translation Protein In higher organisms the picture is a bit more complex. DNA -> pre-mRNA -> mRNA ->protein Protein might need a chaperone in order to fold correctly. movie

5. Subcellular location An animal cell:

6. Proteins - where are they found 1.Proteins are found in all living organisms 2.In humans there are approx 25.000 proteins 3.Each protein has a specific function 1.Making up the human tissue - skin, hair, heart... 2.Degrading the food we eat 3.Immune system 4.Transportation of Oxygen in blood 5.Triggering the growth of cells 6.The brain - neural signalling 4.Typically a protein is approx 220 aa in human 5.Proteins talk, i.e. Protein-protein interactions 1.To relay a signal across the cell-membrane

7. 1 and 3-letter codes 1.There are 20 naturally occurring amino acids 2.Normally the one/three codes are used Ala - A Cys - C Asp - D Glu - E Phe - F Gly - G His - H Ile - I Lys - K Leu - L Met - M Asn - N Pro - P Gln - Q Arg - R Ser - S Thr - T Val - V Trp - W Tyr - Y

8. Graphic stick representation Different aa, different property Ile - Hydrophobic Phe - Hydrophobic & aromatic

9. The 20 amino acids

10. Charged amino acids (sidechain in red) Arg - R Lys - K Asp - D Glu - E His - H

11. Neutral amino acids Ile - I Leu - L Met - M Phe - F Pro - P

12. Property of amino acids (I) neutral, polar or charged ? Ala - A Asn - N Cys - C Gln - Q Gly - G

13. Property of amino acids (II) neutral, polar or charged ? Ser - S Thr - T Trp - W Tyr - Y Val - V

14. Protein structure Primary structure: Amino acids sequences Secondary structure: Helix/Beta sheet Tertiary structure: Fold, 3D cordinates

15. Protein structure  -helix    helix3 residues/turn - few, but not uncommon  - helix3.6 residues/turn - by far the most common helix Pi-helix4.1 residues/turn - very rare

16. Protein structure  strand/sheet

17. Protein structure Ribbon representation - easy to see the secondary structure elements

18. Protein structure

19. Protein structure Hydrophilic/hydrophobic & stacking

20. Protein folds Class 4’th is ‘few secondary structure Architecture Overall shape of a domain Topology Share secondary structure connectivity

21. Summary DNA -> mRNA -> Protein transcription translation 1.20 naturally occurring amino acids 2.Each amino acid has different properties, but can be grouped into: 1.Charged, neutral, polar (basic, acidic) 3.Secondary structure  -helix &  -strand/  -sheet 4.Protein hydrophobic inside, polar on the outside 5.Folds or classes: all , all ,  + , few secondar structure elements

22. Summary The amino acids A - Ala C -Cys D -Asp E -Glu F - Phe G -Gly H -His I -Ile K -Lys M -Met N -Asn P -Pro Q -Gln R -Arg S -Ser T -Thr V -Val W -Trp Y -TyrL -Leu